[gmx-users] error while executing grompp

[Chanchal]

Hi Justin,
  I am still getting the error message : Back Off! I just backed up
mdout.mdp to ./#mdout.mdp.2#
checking input for internal consistency...
processing topology...
Generated 0 of the 595 non-bonded parameter combinations

-------------------------------------------------------
Program grompp_d, VERSION 4.0.5
Source code file: toppush.c, line: 1273

Fatal error:
[ file topol.top, line 3879 ]:
Atom index (1) in settles out of bounds (1-0).
This probably means that you have inserted topology section "settles"
in a part belonging to a different molecule than you intended to.
In that case move the "settles" section to the right molecule.
-------------------------------------------------------

As you said I added the line #define_FF_CHARMM in ffcharmm.itp. Attached is
the file.
Thanks
Chanchal


On Tue, Aug 25, 2009 at 4:42 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
> Your ffcharmm.itp file lacks a necessary line at the very top:
>
> #define _FF_CHARMM
>
> Without this line, grompp does not know which force field you are using,
> and hence everything breaks down when other .itp files are called.
>
> -Justin
>
> Chanchal wrote:
>
>> Hi,
>>  Attached are the top and itp file I am using. Please help me to fix the
>> problem.
>> Thanks
>> Chanchal
>>
>>
>> On Tue, Aug 25, 2009 at 3:44 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    Chanchal wrote:
>>
>>        Hi All,
>>          I have downloaded pdb file and required .top and .itp file
>>        from the site http://www.bioinf.uni-sb.de/RB/ for DOPC
>>        simulation. Now when I execute the command
>>         grompp_d -f em.mdp -c charmm-s22-100ns.pdb -p topol.top -o
>>        dopc.tpr -e ener.edr -t traj.trr I got the error " Fatal error:
>>        [ file tip3p.itp, line 42 ]:
>>        Atom index (1) in settles out of bounds (1-0).
>>        This probably means that you have inserted topology section
>>        "settles"
>>        in a part belonging to a different molecule than you intended to.
>>        In that case move the "settles" section to the right molecule.
>>        -------------------------------------------------------
>>
>>        Attached is the em.mdp file I am using. Please help me how to
>>        solve this problem.
>>
>>
>>    Please see here:
>>
>>
>> http://oldwiki.gromacs.org/index.php/Errors#Atom_index_.281.29_in_bonds_out_of_bounds
>>
>>    The .mdp file is not the source of the problem; the topology is.  If
>>    you need more help, you'll have to post the relevant section.
>>
>>    -Justin
>>
>>        Thanks
>>        Chanchal
>>
>>
>>
>>  ------------------------------------------------------------------------
>>
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>>
>>    --    ========================================
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>    ========================================
>>    _______________________________________________
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>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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